CI01000001_02274875_02276207 (HOXC4, HOXC4A)


Basic Information

Item Value
gene id CI01000001_02274875_02276207
gene name HOXC4, HOXC4A
gene type coding
species grasscarp (Ctenopharyngodon idella)
category of species economic fish

Chromosome Information

Item Value
chromosome id CI01000001
NCBI id null
chromosome length 13537560
location 2274292 ~ 2276769 (-)
genome version v1_2015/06_NatureGenetics_grasscarp_Genome

Sequence

>CI01000001_02274875_02276207.mRNA
ACGCCAAGTCATAAAATGGCGTGGTAAAATAGCTAGCATAGCATAATGTAGAGTAATTATTAGCATTTGATCCGTTATCGAAGTTTAAATGCGATAACTTATTTTTTTTAATTTTATTTTACGACTAGTACCAATACTGCTATTAGCATATTATTAATAATACTGTTTAAACAATGTAATTAGTGAAACTCTTGTAACGACACAAGTTAACTGAGAAACATCCCTAGGTGTTGTGGCATGATCCGAGAAGATTTGGCCATTGTGTATGAGTGTGTGAGAGAGCGAGAAAGGGGGGAGAGAGAGAGGGAGAGAGAGAGAGAGAGAGAAAGATAGAGAGAGGGATAGAAAGACTGAGAGACTTCGCGGACAATGGCGGAAAATTGAAGGTATATTTGCAAAAGCTGTGGTTCCTTATCCGGGGACTACATCGCCCCATGCCATTGGGCCATCGTATCACGTGGTAAAAGTAACTTTACAGGGTTGCTCGCTAGTAGGAGGGCTTTATGGAGCAGAAAAACGACAAAGCTAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCTTGCGAGGAATATTCGCAAAATAGCTACATTCCCGAACATAGCCCCGAATATTACAGCCGTGCAAGGGACAGTGGCTACCAGCATCACCACCAGGAGTTATACCCTCCGCGGGCAAGCTACCAGGAGCGTCAGTATAACTGTGCAAGCATCCCTGAGCCTGATACTCAAAGAGGACATGGACTTCCTCACGCGGGGCACCTGCTCGGAAAAGGGCAATCTGCCTCATGTGAGCCCCCACCGTTACCCCTGTCTCCTGCCACCCCTCCGGCTGCATCCTCCGCCTGCAATCAAGCCACCCCGGAGCATCCCAACAGCTCAGCCTCTGCCAAACAACCCGTCGTGTACCCATGGATGAAGAAAATTCACGTCAGCACCGTCAACTCTAGTTACAATGGAGCGGAACCCAAGCGGTCTAGAACTGCTTACACTCGCCAGCAAGTCTTAGAATTGGAGAAGGAATTCCACTATAATCGGTACTTAACACGGCGAAGACGTATCGAGATTGCTCATTCCTTGGTCCTCTCGGAGAGGCAAATCAAAATTTGGTTTCAGAACCGCAGGATGAAGTGGAAAAAAGACCATAGGCTGCCAAACACCAAAGTCAGATCCTCGTCCTCCACGGGCATTTCCTCCGGGTCCAACACAAGCTCAGCGGCTGCAGGCGTTGTGGCGGCAGCTTCCACCACTAACACCATGTCAGCCTCCGAGGACCTCTCCGGAACCGAGCGTGGCGAGGATATTACAAGGTTATAAGAGAACTATTTCGAGGAGAGACGGGAAGATCAAATGACTGATTATTTATAAAATATAATATATTTTGTTTTCGTAGGTATCTTGTGCGTAAAGGGGGTTCCTTTAAGTCCACAGTTATATAAAATGCATGTTATATAGCATGGATTATTGCGAATACCTATGGATTCTTTTCTACGCGAAACAGGGTTTAATTTATCGAAAAACTGAATCAATATGATGTTTGTTTGTTTTTGTTTTTTTTCTTTTCATTTTCCAAGAGAAATGTTTTGGGCGAAGCAGGTTATGGACATTTTATTCAAATGTTATTTGTGGGCCTTTCTTTGCCCAGCTGCCAAGGTGAAGTGCACAACGAATCTATTTATTTCTCACTTGAGAGAGCTGGTACGTTTTTTTGTACTGTAAATGAAAAACACTATCGTGGGTATCGATAGAAAAAAATATCTTTGTTTTCTTTAAAAGTAAATCATGCTGTGGGGTTATCTGTCGTATGGAAAGGTTAAGACTTTAAATTATCATTTAGTTTTTTGTTGTGATGGCGTTGTGTTTAGGCTATTAACAGCAGATTGTTGTGAGATGCAATAAA

Function

symbol description
hoxc4a Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in several structures, including margin; nervous system; presumptive paraxial mesoderm; swim bladder bud; and tail bud. Orthologous to human HOXC4 (homeobox C4).
hoxc4 Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in nucleoplasm.

GO:

id name namespace
GO:0043565 sequence-specific DNA binding molecular_function

KEGG:

id description
K09304 HOX_4; homeobox protein HoxA/B/C/D4

RNA

RNA id representative length rna type GC content exon number start site end site
CI01000001_02274875_02276207.mRNA True 1949 mRNA 0.43 2 2274292 2276769

Neighbor

gene id symbol gene type direction distance location
CI01000001_02258523_02262621 NA coding downstream 11189 2258442 ~ 2263103 (-)
CI01000001_02236985_02242725 HOXC1A coding downstream 30299 2236582 ~ 2243993 (-)
CI01000001_02173311_02179118 NA coding downstream 93305 2172770 ~ 2180987 (-)
CI01000001_02159372_02162554 HNRNPA1, ROA1 coding downstream 111738 2159159 ~ 2162554 (-)
CI01000001_02141590_02142836 COPZ1, COPZ1.L, COPZ1-B coding downstream 131306 2141560 ~ 2142986 (-)
CI01000001_02286306_02287855 HOXC5A coding upstream 9494 2286263 ~ 2288002 (-)
CI01000001_02289890_02291109 HOXC6.S, HOXC6, HOXC6BA, HOXC6AB, HOXC6A, HOXC6AA coding upstream 12321 2289090 ~ 2291744 (-)
CI01000001_02301569_02304543 HOXC8, HOXC8AB, HOXC8AA, XHOXC8, HOXC8A, HOXC8BA, HOXC8.S coding upstream 24366 2301135 ~ 2304572 (-)
CI01000001_02305032_02310500 HOXC9, HOXC9A, HOXC9AA, HOXC9AB coding upstream 28233 2305002 ~ 2311082 (-)
CI01000001_02318724_02321379 HOXC10A coding upstream 41955 2318724 ~ 2321379 (-)
G14304 NA non-coding downstream 119409 2154382 ~ 2154883 (-)
G14301 NA non-coding downstream 122836 2151126 ~ 2151456 (-)
G14300 NA non-coding downstream 125355 2148714 ~ 2148937 (-)
G14297 NA non-coding downstream 130927 2143141 ~ 2143365 (-)
G14293 NA non-coding downstream 155726 2118355 ~ 2118566 (-)
G14335 NA non-coding upstream 91089 2367858 ~ 2368107 (-)
G14194 NA non-coding upstream 121386 2398155 ~ 2398918 (-)
G14344 NA non-coding upstream 126408 2403177 ~ 2403748 (-)
G14214 NA non-coding upstream 193426 2470195 ~ 2473589 (-)
G14445 NA non-coding upstream 347538 2624307 ~ 2624520 (-)
G14228 NA other downstream 217814 2055974 ~ 2056478 (-)
G14219 NA other downstream 279394 1994210 ~ 1994898 (-)
G14104 NA other downstream 506834 1763669 ~ 1771468 (-)
CI01000001_00362143_00378213 NA other downstream 1877159 361614 ~ 378213 (-)
CI01000001_00238241_00249437 NA other downstream 2016775 238241 ~ 249437 (-)
CI01000001_04395469_04399381 FKBP1B.L, FKBP1B, FKBP1AA, FKBP1AB, FKBP1A, FKB1B, FKB1A other upstream 2115545 4392314 ~ 4399804 (-)
CI01000001_04468566_04523431 DNMT3BB.1 other upstream 2199515 4468209 ~ 4523431 (-)
CI01000001_04726550_04727511 PDPFB, PPDPFB, PPDPF other upstream 2292313 4725927 ~ 4728210 (-)
G15736 NA other upstream 2524132 4800901 ~ 4801395 (-)
G16332 NA other upstream 2673920 4950689 ~ 4957842 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_021867 hoxc4a coding NC_007134.7 CM002907.2 36130883 ~ 36132563 (+)
bowfin (Amia calva) AMCG00008811 hoxc4 coding CM030126.1 CM030126.1 12504256 ~ 12505029 (+)